Systems biologists often distance themselves from reductionist approaches and formulate their aim as understanding living systems “as a whole.” Yet, it is often unclear what kind of reductionism they have in mind, and in what sense their methodologies would offer a superior approach. To address these questions, we distinguish between two types of reductionism which we call “modular reductionism” and “bottom-up reductionism.” Much knowledge in molecular biology has been gained by decomposing living systems into functional modules or through detailed studies (...) of molecular processes. We ask whether systems biology provides novel ways to recompose these findings in the context of the system as a whole via computational simulations. As an example of computational integration of modules, we analyze the first whole-cell model of the bacterium M. genitalium. Secondly, we examine the attempt to recompose processes across different spatial scales via multi-scale cardiac models. Although these models rely on a number of idealizations and simplifying assumptions as well, we argue that they provide insight into the limitations of reductionist approaches. Whole-cell models can be used to discover properties arising at the interfaces of dynamically coupled processes within a biological system, thereby making more apparent what is lost through decomposition. Similarly, multi-scale modeling highlights the relevance of macroscale parameters and models and challenges the view that living systems can be understood “bottom-up.” Specifically, we point out that system-level properties constrain lower-scale processes. Thus, large-scale modeling reveals how living systems at the same time are more and less than the sum of the parts. (shrink)

We present two case studies from contemporary biology in which we observe conflicts between established and emerging approaches. The first case study discusses the relation between molecular biology and systems biology regarding the explanation of cellular processes, while the second deals with phylogenetic systematics and the challenge posed by recent network approaches to established ideas of evolutionary processes. We show that the emergence of new fields is in both cases driven by the development of high-throughput data generation technologies and the (...) transfer of modeling techniques from other fields. New and emerging views are characterized by different philosophies of nature, i.e. by different ontological and methodological assumptions and epistemic values and virtues. This results in a kind of conflict we call “epistemic competition” that manifests in two ways: On the one hand, opponents engage in mutual critique and defense of their fundamental assumptions. On the other hand, they compete for the acceptance and integration of the knowledge they provide by a broader scientific community. Despite an initial rhetoric of replacement, the views as well as the respective audiences come to be seen as more clearly distinct during the course of the debate. Hence, we observe—contrary to many other accounts of scientific change—that conflict results in the formation of new niches of research, leading to co-existence and perceived complementarity of approaches. Our model thus contributes to the understanding of the pluralization of the scientific landscape. (shrink)

Occam’s razor refers to the idea that among competing explanations the simplest should be preferred. This principle has been understood and defended in different ways. Some systems biologists argue that traditional molecular biology is misguided because it relies on an unjustified application of Occam’s razor. I analyze which version of the principle is relevant in this context and ask whether the allegation stands up to scrutiny by looking at actual research. I defend the traditional approach by arguing that its use (...) of Occam’s razor is innocuous and by showing that systems biology heavily relies on considerations of simplicity as well. (shrink)

The philosophical debate around the impact of machine learning in science is often framed in terms of a choice between AI and classical methods as mutually exclusive alternatives involving difficult epistemological trade-offs. A common worry regarding machine learning methods specifically is that they lead to opaque models that make predictions but do not lead to explanation or understanding. Focusing on the field of molecular biology, I argue that in practice machine learning is often used with explanatory aims. More specifically, I (...) argue that machine learning can be tightly integrated with other, more traditional, research methods and in a clear sense can contribute to insight into the causal processes underlying phenomena of interest to biologists. One could even say that machine learning is not the end of theory in important areas of biology, as has been argued, but rather a new beginning. I support these claims with a detailed discussion of a case study involving gene regulation by microRNAs. (shrink)

- A recent debate has touched upon the question of whether diseases can be understood as dysfunctional mechanisms or whether there are "pathological" mechanisms that deserve to be investigated and explained independently (Nervi 2010; Moghaddam Taaheri 2011). Here I suggest that both views tell us something important about disease but that in many instances only a systemic view can shed light on the relationship between physiology and pathology. I provide examples from the literature in systems biology in support of my (...) position. As a result of my analysis, I conclude that a perspective narrowly focusing on mechanisms is insufficient if the goal is to get a comprehensive picture of disease. (shrink)

Even though complexity is a concept that is ubiquitously used by biologists and philosophers of biology, it is rarely made precise. I argue that a clarification of the concept is neither trivial nor unachievable, and I propose a unifying framework based on the technical notion of “effective complexity” that allows me to do justice to conflicting intuitions about biological complexity, while taking into account several distinctions in the usage of the concept that are often overlooked. In particular, I propose a (...) distinction between two kinds of complexity, “mechanical” and “emergent”, which can be understood as different ways of relating the effective complexity of mechanisms and of behaviors in biological explanations. I illustrate the adequacy of this framework by discussing different attempts to understand intracellular organization in terms of pathways and networks. My framework provides a different way of thinking about recent philosophical debates, for example, on the difference between mechanistic and topological explanations and about the concept of emergence. Moreover, it can contribute to a proper assessment of metascientific arguments that invoke biological complexity. (shrink)

Systems biology is sometimes presented as providing a superior approach to the problem of biological complexity. Its use of ‘unbiased’ methods and formal quantitative tools might lead to the impression that the human factor is effectively eliminated. However, a closer look reveals that this impression is misguided. Systems biologists cannot simply assemble molecular information and compute biological behavior. Instead, systems biology’s main contribution is to accelerate the discovery of mechanisms by applying models as heuristic tools. These models rely on a (...) variety of idealizing and simplifying assumptions in order to be efficient for this purpose. The strategies of systems biologists are similar to those of experimentalists in that they attempt to reduce the complexity of the discovery process. Analyzing and comparing these strategies, or ‘heuristics’, reveals the importance of the human factor in computational approaches and helps to situate systems biology within the epistemic landscape of the life sciences. (shrink)

Cancers rely on multiple, heterogeneous processes at different scales, pertaining to many biomedical fields. Therefore, understanding cancer is necessarily an interdisciplinary task that requires placing specialised experimental and clinical research into a broader conceptual, theoretical, and methodological framework. Without such a framework, oncology will collect piecemeal results, with scant dialogue between the different scientific communities studying cancer. We argue that one important way forward in service of a more successful dialogue is through greater integration of applied sciences (experimental and clinical) (...) with conceptual and theoretical approaches, informed by philosophical methods. By way of illustration, we explore six central themes: (i) the role of mutations in cancer; (ii) the clonal evolution of cancer cells; (iii) the relationship between cancer and multicellularity; (iv) the tumour microenvironment; (v) the immune system; and (vi) stem cells. In each case, we examine open questions in the scientific literature through a philosophical methodology and show the benefit of such a synergy for the scientific and medical understanding of cancer. (shrink)

"Evidence of a flight from reason is as old as human record-keeping: the fact of it certainly goes back an even longer way. Flight from science specifically, among the forms of rational inquiry, goes back as far as science itself... But rejection of reason is now a pattern to be found in most branches of scholarship and in all the learned professions."--from the introduction In the widely acclaimed Higher Superstition: The Academic Left and Its Quarrels with Science, Paul R. (...) class='Hi'>Gross and Norman Levitt offered a spirited response to the "science bashers," raising serious questions about the growing criticism of scientific practice from humanists and social scientists on the academic left. Now, in The Flight from Science and Reason, Gross and Levitt are joined by Martin W. Lewis to bring together a diverse and distinguished group of scholars, scientists, and experts to engage these questions from a wide variety of perspectives. The authors take on critics of science whose views range from moderate to extreme, from social constructivists to deconstructionists, from creationists and feminists to Afro-centrists. They discuss the rise of "alternative medicine" and radical environmentalism (here skewered as "ecosentimentalism"). They explain why the "uncertainty principle" does not work as a metaphor for ambiguity, and why "chaos theory" cannot be invoked without an understanding of mathematics. Throughout, they grapple with the paradox inherent in arguing with opponents who contend that reason itself, and thus logic, is suspect. Distributed for the New York Academy of Sciences. (shrink)

In the present paper, it is shown that Kant in his theory of fine art from the Critique of Aesthetic Judgment proves to be a proponent of aesthetic cognitivism, according to which art is, first, a source of non-trivial knowledge and, second, this knowledge also has aesthetic relevance. This issue has been raised several times in the recent research literature, but has not been substantiated, or only briefly. Central to this is Kant's conception of aesthetic ideas, with which fine art (...) symbolizes intellectual ideas of various genesis and with which his theory of art acquires a content-aesthetic dimension. Discussing recent research literature, an interpretation for the conception of aesthetic ideas and the accompanying expressive dimension of fine art is offered in a first part. Based on this, it will be shown in a second part that Kant hereby proves to be a representative of aesthetic cognitivism; this is shown by the fact that his theory of art confirms both criteria of aesthetic cognitivism. (shrink)

Both trolleys and war leave innocent victims to suffer death and injury. Trolley problems accounting for the injured, and not only the dead, tease out intuitions about liability that enhance our understanding of the obligation to provide compensation and medical care to civilian victims of war. Like many trolley victims, civilians in war may suffer justifiable, excusable, or negligent harms that demand compensation. Chief among these is collateral harm befalling civilians. Collateral harm is endemic to war and comprises permissible but (...) unavoidable death or injury following necessary and proportionate military operations. Although state armies sometimes offer condolence payments for civilian death, injury, and property loss, they deny liability. Instead, they use compensation to enhance counterinsurgency efforts and assuage feelings of agent regret. As part of the medical rules of eligibility, Coalition forces in Iraq and Afghanistan also provided medical care to victims of collateral harm. However, they denied care to similarly sick or injured civilians. While compensation is often justified to cure the harm civilians suffer, the differential use of medical resources is not. Rather, medical care remains subject to the principle of beneficence and medical need. The duty to provide civilian healthcare in war, particularly in wars of humanitarian intervention, is far-reaching and imposes significant costs that military and medical ethics are yet to recognize. (shrink)

ABSTRACT How should physicians act when faced with corporal punishment, such as amputation, or torture? In most cases, the answer is clear: international law, UN resolutions and universal codes of medical ethics absolutely forbid physicians from countenancing torture and corporal punishment in any form. An acute problem arises, however, in decent societies, but not necessarily liberal states, that are, nonetheless, welcome in the world community. The decent society is often governed, in whole or in part, by religious laws, and while (...) these states abridge various human rights they are peace loving, generally tolerant, and offer their citizens wide avenues for political participation. Under these circumstances the prohibition against corporal punishment and torture weakens, often compelling physicians to participate. This is true in two cases. In Rawls’ hypothetical nation of Kazanistan, Islamic law is the order of the day, and amputations and corporal punishment play an integral part in the execution of traditional Islamic justice. In Israel, torture is sometimes used to elicit the information needed to thwart impending terror attacks. In each case, a physician's participation is essential. In light of the near universal condemnation that accompanies torture and corporal punishment, physicians can only appeal to norms anchored in collective well‐being and concern for life that override respect for human dignity in these societies. Western societies have consistently rejected this reasoning, but it is part and parcel of life in the decent society. (shrink)

Zenon Pylyshyn argues that cognitively driven attentional effects do not amount to cognitive penetration of early vision because such effects occur either before or after early vision. Critics object that in fact such effects occur at all levels of perceptual processing. We argue that Pylyshyn’s claim is correct—but not for the reason he emphasizes. Even if his critics are correct that attentional effects are not external to early vision, these effects do not satisfy Pylyshyn’s requirements that the effects be direct (...) and exhibit semantic coherence. In addition, we distinguish our defense from those found in recent work by Raftopoulos and by Firestone and Scholl, argue that attention should not be assimilated to expectation, and discuss alternative characterizations of cognitive penetrability, advocating a kind of pluralism. (shrink)

ABSTRACT How should physicians act when faced with corporal punishment, such as amputation, or torture? In most cases, the answer is clear: international law, UN resolutions and universal codes of medical ethics absolutely forbid physicians from countenancing torture and corporal punishment in any form. An acute problem arises, however, in decent societies, but not necessarily liberal states, that are, nonetheless, welcome in the world community. The decent society is often governed, in whole or in part, by religious laws, and while (...) these states abridge various human rights they are peace loving, generally tolerant, and offer their citizens wide avenues for political participation. Under these circumstances the prohibition against corporal punishment and torture weakens, often compelling physicians to participate. This is true in two cases. In Rawls’ hypothetical nation of Kazanistan, Islamic law is the order of the day, and amputations and corporal punishment play an integral part in the execution of traditional Islamic justice. In Israel, torture is sometimes used to elicit the information needed to thwart impending terror attacks. In each case, a physician's participation is essential. In light of the near universal condemnation that accompanies torture and corporal punishment, physicians can only appeal to norms anchored in collective well‐being and concern for life that override respect for human dignity in these societies. Western societies have consistently rejected this reasoning, but it is part and parcel of life in the decent society. (shrink)

A survey of innateness in cognitive science, focusing on (1) what innateness might be, and (2) whether concepts might be innate.

The malicious acts of terrorism in New York and Washington emphasized the need for states to combat terrorism. Likewise, Israel has suffered various terrorist attacks since its establishment. There are distinctive features in contemporary terrorism which call for a new assessment of its nature and the status of terrorists in domestic and international law. In October 2000, a violent conflict erupted between organizations operating within the territory of the Palestinian Authority--an entity that is not a state but is a sovereign (...) authority--and the State of Israel. This is a new type of armed conflict, one different from that treated in the international law of armed conflicts. No clear view exists as to the rules which should be applied in such a situation. This is one of the questions that shall be raised in this article. As a result of the violence against Israel, Israel initiated a policy which the media has called 'Israel's elimination policy', but which I believe may be more appropriately described as 'preventive action' taken by Israel within the framework of a military policy aimed at neutralizing terrorist organizations by targeting the perpetrators or their commanders. In this article I shall examine whether this policy is legitimate as a matter of law and morality. (shrink)

We are often told that we are morally obligated to produce equal opportunity for all. Therefore, it seems we should examine what power we have to produce that desirable state. For it would be nonsense to say we are required to provide what is beyond our power to provide. When we examine this question, we find our power limited by two sets of constraints. One set comprises formal constraints upon the idea itself of equal opportunity. We cannot do the logically (...) impossible. The other set comprises limits upon our ability to produce the directed socio-economic change, getting known outputs for known inputs. I illustrate the formal constraints by outlining the work of Douglas Rae. The constraints upon our abilities I illustrate with evidence from sociology and politics. At the end, we shall discover that our power to make opportunities equal is sharply though not unbearably limited. A critical but unbaised survey will reveal that in the past fifty years we have gone remarkably far towards doing all that we are presently capable of doing to equalize opportunities. Perhaps we shall go even farther when we learn how. The word ‘real’ in the title is opposed to ‘ideal’ or even ‘chimerical'. It may seem an interesting question what equality of opportunity should consist in were we able to produce directed socio-economic change at will. But we are not. Therefore, a more interesting and more important question is what equality of opportunity consists in given the very large number of constraints within which we must work to achieve it. (shrink)

Catholic thinkers generally agree that artificial womb technology (AWT) would be permissible in cases of partial ectogenesis to assist severely premature infants, but there is substantially more debate concerning whether AWT could be used to save frozen embryos, which are the result of in vitro fertilization (IVF). In many cases, these embryos have been abandoned and left in a permanently cryogenic state, which is an affront to their human dignity. While AWT would allow people to adopt these embryos and give (...) them an opportunity to develop, it gives rise to serious concerns over the possibility of scandal and the potential for cooperation in evil. Therefore, the author argues that even though AWT may one day represent a solution to this tragedy, it is currently not a morally licit answer, given the widespread use and approval of IVF in our culture. (shrink)

Ever since Democritus of Abdera (460-370 B.c.E.) introduced the concept of atoms in Western thought, later to be elaborated by Epicuros (as transmitted by Diogenes Laertius) and Lucretius, it lay at the basis of materialistic and atheist world views. Therefore, it may be less surprising to know that as late as 1624 in France, the teaching of atomism was a crime punishable by death. Even when atoms had been accepted, after the time of John Dalton (1766-1844), and indeed were considered (...) indispensable by chemists, resistance against them continued among many physicists. Ludwig Boltzmann, who derived the laws of thermodynamics from the hypothetical existence of "atoms" was the foremost advocate of atomism in the nineteenth century, while another Austrian, Ernst Mach, was its most prominent opponent. Einstein’s first articles were entirely within the Boltzmann tradition. As he explained in his autobiography, his work on fluctuations and Brownian motion was undertaken because of his desire to guarantee the existence of atoms of definite finite size. Boltzmann’s statistical methods were also used by Max Planck for the quantum hypothesis of light, so &dquo;both roots of quantum theory, the Planck root and the Einstein root, go back to Boltzmann&dquo; (Boltzmann, 1981). (shrink)

This book describes the development of the scientific article from its modest beginnings to the global phenomenon that it has become today. The authors focus on changes in the style, organization, and argumentative structure of scientific communication over time. This outstanding resource is the definitive study on the rhetoric of science.

Moving back and forth between the history of philosophy and the contributions of philosophers in his own day, Durkheim takes up topics as diverse as philosophical psychology, logic, ethics, and metaphysics, and seeks to articulate a unified philosophical position. Remarkably, in these lectures, given more than a decade before the publication of his groundbreaking book, The Division of Labour in Society, the 'social realism' that is so characteristic of his later work - where he insists, famously, that social facts cannot (...) be reduced to psychological or economic ones, and that such facts constrain human action in important ways - is totally absent in these early lectures. For this reason, they will be of special interest to students of the history of the social sciences, for they shed important light on the course of Durkheim's intellectual development. (shrink)

Writing about the intellectual development of a philosopher is a delicate business. My own endeavor to reinterpret the influence of Hegel on Dewey troubles some scholars because, they believe, I make Dewey seem less original.1 But if, like Dewey, we overcome Cartesian dualism, placing the development of the self firmly within a complex matrix of social processes, we are forced to reexamine, without necessarily surrendering, the notion of individual originality, or what Neil Gross calls “discourse[s] of creative genius.”2 To (...) use a mundane example, I can recall several conversations with Dewey scholars about his dislike for his home state of Vermont, all of which revolved around personal reasons he may.. (shrink)

Unlike most Western nations, Israel does not recognize full separation of church and state but seeks instead a gentle fusion of Jewish and democratic values. Inasmuch as important religious norms such as sanctity of life may clash with dignity, privacy, and self-determination, conflicts frequently arise as Israeli lawmakers, ethicists, and healthcare professionals attempt to give substance to the idea of a Jewish-democratic state. Emerging issues in Israeli bioethics—end-of-life treatment, fertility, genetic research, and medical ethics during armed conflict—highlight this conflict vividly.

Although the abortion debate continues to simmer in many places, the general issue of a woman's right to an abortion, at least in the Western democracies, is largely settled. In its place, the question of late-term abortion begins to assume a prominence only recently attributed to abortion itself. The advent of sophisticated fetal screening techniques makes possible detection of potentially severe fetal anomalies that in many cases are detected only late in the pregnancy, resulting in the need for late-term abortion.

It is a frequent assumption that—via superluminal information transfers—superluminal signals capable of enabling communication are necessarily exchanged in any quantum theory that posits hidden superluminal influences. However, does the presence of hidden superluminal influences automatically imply superluminal signalling and communication? The non-signalling theorem mediates the apparent conflict between quantum mechanics and the theory of special relativity. However, as a ‘no-go’ theorem there exist two opposing interpretations of the non-signalling constraint: foundational and operational. Concerning Bell’s theorem, we argue that Bell employed (...) both interpretations, and that he finally adopted the operational position which is associated often with ontological quantum theory, e.g., de Broglie–Bohm theory. This position we refer to as “effective non-signalling”. By contrast, associated with orthodox quantum mechanics is the foundational position referred to here as “axiomatic non-signalling”. In search of a decisive communication-theoretic criterion for differentiating between “axiomatic” and “effective” non-signalling, we employ the operational framework offered by Shannon’s mathematical theory of communication, whereby we distinguish between Shannon signals and non-Shannon signals. We find that an effective non-signalling theorem represents two sub-theorems: Non-transfer-control theorem, and Non-signification-control theorem. Employing NTC and NSC theorems, we report that effective, instead of axiomatic, non-signalling is entirely sufficient for prohibiting nonlocal communication. Effective non-signalling prevents the instantaneous, i.e., superluminal, transfer of message-encoded information through the controlled use—by a sender-receiver pair —of informationally-correlated detection events, e.g., in EPR-type experiments. An effective non-signalling theorem allows for nonlocal quantum information transfer yet—at the same time—effectively denies superluminal signalling and communication. (shrink)

Modern war poses hard ethical problems for the practice of medicine, making it difficult to identify medical ethics during times of armed conflict with medical ethics during times of peace. This sets up an enduring challenge for medicine, as doctors and other healthcare professionals weigh their responsibilities as caregivers against other responsibilities and obligations that citizens must shoulder during war.

Communities are the chief source of philosophical sloppiness these days. Varying endlessly across the entire range of human experience, communities raise the specter of moral relativism that makes ethics sometimes seem a misguided and futile enterprise. Yet the language of communities and their multitude of norms, preferences, and principles present an opportunity, and challenge, to confront abiding moral problems in immeasurably richer and more novel ways. But neither the opportunities nor the challenges were always obvious. On the contrary, the origins (...) of the Enlightenment coincide with an assault on the disharmony posed by restless and unruly communities. (shrink)